Using a Centroid-based approach for a reliable identification of morels (Morchella spp.): A case study for food authentication.

Food fraud is a problematic yet common phenomenon in the food industry. It impacts numerous sectors, including the market of edible mushrooms. Morel mushrooms are prized worldwide for their culinary and medicinal use. They represent a taxonomically complex group in which food fraud has already been reported. Among the methods to evaluate food fraud, some rely on comparisons of genetic sequences obtained from a sample to existing databases. However, the quality and usefulness of the results are limited by the type of comparison tool and the quality of the database used. The Centroid-based approach is applied by SmartGene in a proprietary artificial intelligence-based method for the generation of automatically curated reference databases that can be further expert curated. In this study, using sequences of the ribosomal internal transcribed spacer (ITS) of the genus Morchella (true morels), we compared this approach to the traditional pairwise alignment tool using two other databases: UNITE and Mycobank (MLST). The Centroid-based approach using an expert-curated database was more performant for the identification of 53 representative ITS sequences corresponding to validated species (83% accuracy, compared to 36% and 47% accuracy for UNITE and MLST, respectively). The Centroid method also revealed an inaccurate taxonomic annotation for sequences of commercial cultivars submitted to public databases. Combined with the web-based commercial software IDNS® available at Smartgene, the Centroid-based approach constitutes a valuable tool to ensure the quality of morel products on the market for actors of the food industry. PRACTICAL APPLICATION: The Centroid-based approach can be used by agri-food actors who need to identify true morels down to the species level without any prior taxonomical knowledge. These include routine laboratories of the food industry, food distributors, and public surveillance agencies. This is a reliable method that requires minimal skills and resources, therefore being particularly adapted for nonspecialists.

Gamification as a tool to teach key concepts in microbiology to bachelor-level students in biology: a case study using microbial interactions and soil functioning.

Microbiology is a difficult topic to teach given that the objects of study are mostly invisible to the learner. The majority of university students beginning their training in biology are more interested in natural objects that can be seen with the naked eye. Nonetheless, micro-organisms are key components of the biosphere and a good microbiological background is required for a thorough training in natural sciences. Lectures are still a common teaching format in universities. However, it is a passive learning format and no longer considered the most adequate approach in most teaching situations. Instead, alternatives consisting of more active teaching formats have been recognized to better motivate students to acquire and consolidate knowledge. In addition, transferable skills, such as effective communication, critical thinking and time management, are acquired simultaneously. A similar engagement can be obtained using games as part of the teaching experience. In this study, we designed a card game to teach key concepts in basic bacteriology and mycology to bachelor-level students. The first task consists of creating and designing microbial characters based on a list of species. This proved very useful for second-year bachelor students in terms of grasping concepts such as cell morphologies, taxonomy and life cycles. In the second task, third-year students used the characters created in the second-year class to develop a game based on an ecological function, namely forest litter degradation. In addition, they also considered experimental validation of the microbial activities and incorporated knowledge acquired in other fields.

Associated bacterial communities, confrontation studies, and comparative genomics reveal important interactions between Morchella with Pseudomonas spp.

Members of the fungal genus Morchella are widely known for their important ecological roles and significant economic value. In this study, we used amplicon and genome sequencing to characterize bacterial communities associated with sexual fruiting bodies from wild specimens, as well as vegetative mycelium and sclerotia obtained from Morchella isolates grown in vitro. These investigations included diverse representatives from both Elata and Esculenta Morchella clades. Unique bacterial community compositions were observed across the various structures examined, both within and across individual Morchella isolates or specimens. However, specific bacterial taxa were frequently detected in association with certain structures, providing support for an associated core bacterial community. Bacteria from the genus Pseudomonas and Ralstonia constituted the core bacterial associates of Morchella mycelia and sclerotia, while other genera (e.g., Pedobacter spp., Deviosa spp., and Bradyrhizobium spp.) constituted the core bacterial community of fruiting bodies. Furthermore, the importance of Pseudomonas as a key member of the bacteriome was supported by the isolation of several Pseudomonas strains from mycelia during in vitro cultivation. Four of the six mycelial-derived Pseudomonas isolates shared 16S rDNA sequence identity with amplicon sequences recovered directly from the examined fungal structures. Distinct interaction phenotypes (antagonistic or neutral) were observed in confrontation assays between these bacteria and various Morchella isolates. Genome sequences obtained from these Pseudomonas isolates revealed intriguing differences in gene content and annotated functions, specifically with respect to toxin-antitoxin systems, cell adhesion, chitinases, and insecticidal toxins. These genetic differences correlated with the interaction phenotypes. This study provides evidence that Pseudomonas spp. are frequently associated with Morchella and these associations may greatly impact fungal physiology.

Importance of appropriate genome information for the design of mating type primers in black and yellow morel populations.

Morels are highly prized edible fungi where sexual reproduction is essential for fruiting-body production. As a result, a comprehensive understanding of their sexual reproduction is of great interest. Central to this is the identification of the reproductive strategies used by morels. Sexual reproduction in fungi is controlled by mating-type (MAT) genes and morels are thought to be mainly heterothallic with two idiomorphs, MAT1-1 and MAT1-2. Genomic sequencing of black (Elata clade) and yellow (Esculenta clade) morel species has led to the development of PCR primers designed to amplify genes from the two idiomorphs for rapid genotyping of isolates from these two clades. To evaluate the design and theoretical performance of these primers we performed a thorough bioinformatic investigation, including the detection of the MAT region in publicly available Morchella genomes and in-silico PCR analyses. All examined genomes, including those used for primer design, appeared to be heterothallic. This indicates an inherent fault in the original primer design which utilized a single Morchella genome, as the use of two genomes with complementary mating types would be required to design accurate primers for both idiomorphs. Furthermore, potential off-targets were identified for some of the previously published primer sets, but verification was challenging due to lack of adequate genomic information and detailed methodologies for primer design. Examinations of the black morel specific primer pairs (MAT11L/R and MAT22L/R) indicated the MAT22 primers would correctly target and amplify the MAT1-2 idiomorph, but the MAT11 primers appear to be capable of amplifying incorrect off-targets within the genome. The yellow morel primer pairs (EMAT1-1 L/R and EMAT1-2 L/R) appear to have reporting errors, as the published primer sequences are dissimilar with reported amplicon sequences and the EMAT1-2 primers appear to amplify the RNA polymerase II subunit (RPB2) gene. The lack of the reference genome used in primer design and descriptive methodology made it challenging to fully assess the apparent issues with the primers for this clade. In conclusion, additional work is still required for the generation of reliable primers to investigate mating types in morels and to assess their performance on different clades and across multiple geographical regions.